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Once the Joker had control of the city, he reported that if anyone is still in the city by nightfall, they will subject to his rule. However, he also warned the city of the bridges and the tunnels having explosives, which lead to the city taking two boats to escape, believing there would be no harm done there. The citizens were on one boat, and the criminals were on the other. However, the Joker revealed that there are two bombs on each boat and each boat has a detonator to the other. He gave them an ultimatum: if neither the citizens or the criminals blow the other up by midnight, the Joker will blow up both ships.

After Batman discovered the location of the Joker, he arrived at the Prewitt Building and began to attack who he believed were the thugs. However, he realized that the hostages were the Joker's men and the Joker's men were actually the hostages. The SWAT team eventually discovered this as well and started arresting the mob while Batman left to confront the Joker.

Upon meeting the Joker, Batman demands to know the location of the detonator. Joker replies by letting The Chechen's vicious dogs off their leash and then proceeds to rush Batman, swinging wildly with a pipe in an attempt to incapacitate our hero while he was distracted by the Rottweiler attack. From his back, Batman manages to send Joker to the floor with a kick to the chest, successfully repelling the attempted assault only to see the Joker immediately get to his feet and resume swinging. When Batman successfully fends off the second attack, Joker disappears, stepping into the shadows while Batman finally forces the dogs into submission.

Upon getting back to his feet, Batman engages his sonar vision in an attempt to locate the Joker only to notice a moment too late that the villain had unexpectedly bum-rushed him, landing a direct blow from his pipe to Batman's head. The successful attack sent Batman sliding across the floor in the direction of the window overlooking the water where the twin ferry boats sat. Joker wasted no time after the successful attack, mounting Batman and pinning him to the floor where he had slid to a stop, pressing his pipe to Batman's chest.

While in the dominant position with a perfect view of the ferry boats below, Joker exclaimed excitedly that they were about to witness an explosion, glancing with anticipation at his wrist watch. When the deadline passed (which Joker had set for the inhabitants of either boat to detonate the other) without either side having the constitution for murder, he angrily produced his own detonator, preparing to kill the inhabitants of both boats as punishment for disappointing him. Joker then began explaining to Batman the origin of his scars as his thumb began the descent to the detonator's button, but he was thwarted in his attempt when Batman, utilizing the leverage afforded to him by the weight Joker was applying to keep him pinned, rolled his legs up over his head and threw the Joker from the open window, sending him speeding toward the concrete below.

Believing he'd finally forced Batman to kill, the Joker began maniacally laughing only to be disappointed yet again when a grapnel gun wire wrapped around his legs, saving his life. At the other end of that wire, Batman was hoisting the villain back to the window from which he'd thrown him, bringing his inverted assailant back to eye level. When their eyes finally met, Joker acknowledged for the first time that Batman truly is incorruptible.

Once the Joker informed Batman that he had convinced Harvey Dent to take revenge on the people responsible for Rachel's death, the Batman left to find Harvey at the building where Rachel died. He tried to reason with Harvey, but Harvey decided to flip his coin for Batman, himself, and Gordon's son. The coin landed on its scarred side and Harvey shot him and he fell. It was Harvey's turn, and the coin landed on the unscarred side of the coin. Before he can determine Gordon's son's fate, Batman threw himself at Dent and saved Gordon's son and soon fell to the ground himself. Once Gordon came to help Batman up, it was then that they discovered Harvey had died from the fall. Now concerened with Harvey's reputation, Gordon realises that the Joker succeeded in destroying Gotham by making them lose hope in saving Gotham. But Batman decides to save Dent's image by making himself responsible for the lives Dent took. Gordon had no other choice and had to issue a manhunt on Batman- thus, no matter what happened, the Joker inflicted a final, permanent scar on Batman's career.